How do I change the default settings?

The Biognosys Factory Settings or default settings are suitable for most experimental setups. However, sometimes non‑default settings are necessary or preferred. The process described below is applicable to any Biognosys software, although the screenshots shown here are taken from Spectronaut.

You can change the default settings in three ways:

Creating and saving your own settings schema

Open the software and go to the Settings Perspective (see Figure 1). You will find several tabs, each corresponding to the various processes you can run in the software. For example, if you are performing a data independent acquisition (DIA) analysis in Spectronaut, go to the DIA analysis page and select one of the schemas, e.g. the BGS Factory Settings (default) schema. On the second level, you can see the different aspects of the analysis. On the third level you can finally see and edit the settings. If you hover over each, a brief explanation pops up. Some settings will be shown only if the higher-class check-box is checked, like with Generate Decoys on Figure 1.

Figure 1. Exploring the Settings Perspective

Once you have edited the schema with your ideal settings, save it by clicking on Save As in the bottom-left corner, give it a name and click OK (see Figure 2). Now you will see your custom schema listed under Schemas. Unlike the BGS Factory Settings (default) schema, created schemas can be removed and edited.

 

Figure 2. Saving and naming the new schema

Changing the settings on the go

When you start an analysis in the Analysis Perspective (Monitor in QuiC), you can change the default settings in the Experiment Setup window (see Figure 3). For each aspect of the analysis, you can choose your preferred settings. Click Finish when the experiment has been configured. In this case, the changes will only apply to the ongoing analysis and won’t be saved for future setups.

 

Figure 3. Changing the analysis settings in the Experiment Setup window

Recalculating an already analyzed dataset (not applicable to QuiC)

In the Analysis Perspective, right click on the experiment tab and choose Settings. Additionally, in Spectronaut software you can find convenient icons that comprise shortcut to settings and other analysis functions (Figure 4). Now, at the bottom half of the window, you can see the Analysis Settings (Figure 5). Similarly, to point number 2, for each aspect of the analysis, you can choose your preferred settings. Click Confirm to start recalculating. 

Figure 4. Changing the settings to an already analyzed dataset

Figure 5. Choosing your preferred settings to recalculate the analysis

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